South Korea's navy has fired warning shots towards North Korean fishing boats that crossed a disputed maritime boundary, a South Korean official said.

No North Korean navy ships were involved in the incident on Friday along a western sea boundary that North Korea has long refused to recognise, an official with South Korea's joint chiefs of staff said, speaking anonymously because of office policy.

The shots did not hit the fishing boats, which then retreated, the official added.

Violence often erupts in the seafood-rich Yellow Sea waters claimed by both countries. Boats routinely jostle for position during crab-catching season, and three deadly naval clashes since 1999 have resulted in a few dozen deaths. The disputed sea boundary is not clearly marked, and incursions by North Korean military and fishing boats are not unusual.

Last week, North Korean fishing boats crossed the boundary but retreated soon after being warned by South Korea. Seoul says North Korean fishing boats also crossed the boundary in April.

The Korean war ended nearly 60 years ago with a truce, not a peace treaty, so the US-led UN Command divided the Yellow Sea without Pyongyang's consent. The boundary favoured South Korea, cutting off North Korea from rich fishing waters and boxing in one of its crucial deep-water ports. North Korea has contested the line ever since, arguing it should run farther south. But for Seoul, accepting such a line would endanger fishing around five South Korean islands and hamper access to its port at Incheon.

In 2010, a North Korean artillery barrage on Yeonpyeong Island, which is near the boundary, killed four South Koreans, including two civilians. The same year an explosion ripped apart a South Korean warship in the area, killing 46 sailors. Seoul says Pyongyang torpedoed the vessel. North Korea denies responsibility.